FAPESP also invests in research which, in addition to the advancement of knowledge, has economic or social interest and clear application objectives. The following programs are focused on research with an applied objective:
- Virtual Biodiversity Institute (Biota)
- Program for Research on Bioenergy (BIOEN)
- Research Program on Global Climate Change (RPGCC)
- Inter-institutional Cooperation in Support of Brain Research (CInAPCe)
- Information Technology and the Development of Advanced Internet (Tidia)
- Improvement in Public Education
- Scientific Journalism – Media Science
- Programs for Research in Public Policies
- Research in Public Policies (PP)
- Research in Public Policies for the National Health System (PP-SUS), within an agreement with the State of São Paulo Health Secretary and the Ministry of Health
- Programs for Cooperative University-Industry Research
- Research Partnership for Technological Innovation (PITE)
- Innovative Research in Small Businesses (PIPE)
- Support for Intellectual Property (PAPI-Nuplitec)